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(-) Description

Title :  THE STRUCTURE OF PHYCOCYANIN FROM GLOEOBACTER VIOLACEUS
 
Authors :  J. W. Murray, S. Benson, J. Nield, J. Barber
Date :  12 Dec 07  (Deposition) - 25 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (6x)
Keywords :  Photosynthesis, Light Harvesting (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. W. Murray, S. Benson, J. Nield, J. Barber
The Structures Of The Phycobiliproteins Of Gloeobacter Violaceus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHYCOCYANIN ALPHA CHAIN
    Chains: A
    Organism Scientific: GLOEOBACTER VIOLACEUS
    Organism Taxid: 33072
    Other Details: PASTEUR CULTURE COLLECTION
    Strain: PCC7421
 
Molecule 2 - PHYCOCYANIN BETA CHAIN
    Chains: B
    Organism Scientific: GLOEOBACTER VIOLACEUS
    Organism Taxid: 33072
    Other Details: PASTEUR CULTURE COLLECTION
    Strain: PCC7421

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (6x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1CYC3Ligand/IonPHYCOCYANOBILIN
Biological Unit 1 (1, 18)
No.NameCountTypeFull Name
1CYC18Ligand/IonPHYCOCYANOBILIN

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:60 , LEU A:66 , MET A:72 , GLY A:73 , ASN A:78 , LYS A:81 , CYS A:82 , ARG A:84 , ASP A:85 , HIS A:88 , TYR A:89 , TYR A:108 , PHE A:120 , LEU A:122 , TRP A:126 , TYR A:127 , HOH A:2039 , HIS B:57 , ILE B:67 , TYR B:74 , PRO B:75 , ASN B:76 , HOH B:2017BINDING SITE FOR RESIDUE CYC A1082
2AC2SOFTWAREASN B:72 , ALA B:73 , ARG B:77 , ARG B:78 , ALA B:81 , CYS B:82 , ARG B:84 , ASP B:85 , ILE B:88 , ARG B:108 , LEU B:120 , SER B:126 , VAL B:127 , HOH B:2045BINDING SITE FOR RESIDUE CYC B1082
3AC3SOFTWAREASN A:21 , LEU A:24 , ASN A:28 , ARG A:33 , GLN A:145 , ASN B:35 , LYS B:36 , LEU B:38 , ASP B:39 , VAL B:142 , ASN B:143 , PRO B:145 , VAL B:148 , THR B:149 , ARG B:150 , GLY B:151 , CYS B:153BINDING SITE FOR RESIDUE CYC B1153

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VJR)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr B:74 -Pro B:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VJR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VJR)

(-) Exons   (0, 0)

(no "Exon" information available for 2VJR)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:162
 aligned with Q7M7F7_GLOVI | Q7M7F7 from UniProtKB/TrEMBL  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         Q7M7F7_GLOVI     1 MKTVITEVIASADSQGRFLNNTELQAANGRFQRATASMEAARALTSNADSLVKGAVQEVYNKFPYLTQPGQMGYGDTNQAKCARDISHYLRFITYSLVAGGTGPLDDYIVAGLREVNRTFNLSPSWYIEALKHIKGKVGSQLSGQPLTEANAYIDYCINALS 162
               SCOP domains d2vjra_ A: automated matches                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----Phycobilisome-2vjrA01 A:6-162                                                                                                                                 Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vjr A   1 MKTVITEVIASADSQGRFLNNTELQAANGRFQRATASMEAARALTSNADSLVKGAVQEVYNKFPYLTQPGQMGYGDTNQAKCARDISHYLRFITYSLVAGGTGPLDDYIVAGLREVNRTFNLSPSWYIEALKHIKGKVGSQLSGQPLTEANAYIDYCINALS 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  


Chain B from PDB  Type:PROTEIN  Length:172
 aligned with Q7M7C7_GLOVI | Q7M7C7 from UniProtKB/TrEMBL  Length:172

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
         Q7M7C7_GLOVI     1 MQDAFTKAIVAADLRGSFLSEQELNQLTNLVKESNKRLDAVNAITGNAAEIISDAAHKLFAEQTDLIRPGGNAYPNRRMAACLRDMEIILRYVSYALLAGDASVLEDRCLNGLKETYVALGTPTRSVARAVQLMKETAIGYVNSPSGVTRGDCSALVNEAATYFDKAAASIA 172
               SCOP domains d2vjrb_ B: automated matches                                                                                                                                                 SCOP domains
               CATH domains 2vjrB00 B:1-172 Phycocyanins                                                                                                                                                 CATH domains
               Pfam domains -----Phycobilisome-2vjrB01 B:6-172                                                                                                                                           Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vjr B   1 MQDAFTKAIVAADLRGSFLSEQELNQLTNLVKESNKRLDAVNAITGNAAEIISDAAHKLFAEQTDLIRPGGNAYPNRRMAACLRDMEIILRYVSYALLAGDASVLEDRCLNGLKETYVALGTPTRSVARAVQLMKETAIGYVNSPSGVTRGDCSALVNEAATYFDKAAASIA 172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Globin (291)

(-) Gene Ontology  (4, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q7M7F7_GLOVI | Q7M7F7)
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
    GO:0030089    phycobilisome    Any of the granules, approximately 32 nm x 48 nm and consisting of highly aggregated phycobiliproteins, that are attached in arrays to the external face of a thylakoid membrane in algae of the phyla Cyanophyta and Rhodophyta, where they function as light-harvesting devices in photosynthesis. Excitation energy in the phycobilisome flows in the sequence: phycoerythrin, phycocyanin, allophycocyanin before passing to the antenna chlorophyll of photosystem II.

Chain B   (Q7M7C7_GLOVI | Q7M7C7)
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
    GO:0030089    phycobilisome    Any of the granules, approximately 32 nm x 48 nm and consisting of highly aggregated phycobiliproteins, that are attached in arrays to the external face of a thylakoid membrane in algae of the phyla Cyanophyta and Rhodophyta, where they function as light-harvesting devices in photosynthesis. Excitation energy in the phycobilisome flows in the sequence: phycoerythrin, phycocyanin, allophycocyanin before passing to the antenna chlorophyll of photosystem II.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        Q7M7C7_GLOVI | Q7M7C7: 2vml
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